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So when i am debugging and my vbscript comes across a Wscript.StdIn line a window pops up asking for input. But when i run the script normally in PrimalScript i see the wscript.echo commands in the output window asking for input but there doesn't seem to be a way to enter in input for the Wscript.StdIn command. Am i missing something?

The debugger has a special host to allow debugging scripts that require input, otherwise it wouldn't be much use
However, when you run a script it runs it with the standard CScript.exe. Most scripts only produce output and that is captured and conveyed into the output window.